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Samo Penic

2014-12-16 6bc95bfe19012a33f185adf1476e623d98d33465

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88f451	1	#include<math.h>
SP	2	#include<stdlib.h>
	3	#include "general.h"
	4	#include "sh.h"
267db5	5	#include "io.h"
SP	6	#include <string.h>
074a17	7
fda1ab	8	/* do not use!!! */
074a17	9	ts_spharm sph_init(ts_vertex_list vlist, ts_uint l){
eb8605	10	ts_uint j,i;
074a17	11	ts_spharm sph=(ts_spharm )malloc(sizeof(ts_spharm));
SP	12
262607	13	sph->N=0;
eb8605	14	/* lets initialize Ylm for each vertex. */
SP	15	sph->Ylmi=(ts_double *)calloc(l,sizeof(ts_double ));
5bb11d	16	for(i=0;i<l;i++){
SP	17	sph->Ylmi[i]=(ts_double *)calloc(2i+1,sizeof(ts_double *));
	18	for(j=0;j<(2*i+1);j++){
eb8605	19	sph->Ylmi[i][j]=(ts_double *)calloc(vlist->n,sizeof(ts_double));
074a17	20	}
SP	21	}
	22
	23	/* lets initialize ulm */
	24	sph->ulm=(ts_double *)calloc(l,sizeof(ts_double ));
	25	for(j=0;j<l;j++){
	26	sph->ulm[j]=(ts_double )calloc(2j+1,sizeof(ts_double));
	27	}
	28
262607	29	/* lets initialize sum of Ulm2 */
SP	30	sph->sumUlm2=(ts_double *)calloc(l,sizeof(ts_double ));
	31	for(j=0;j<l;j++){
	32	sph->sumUlm2[j]=(ts_double )calloc(2j+1,sizeof(ts_double));
	33	}
074a17	34
SP	35	/* lets initialize co */
79fc9c	36	//NOTE: C is has zero based indexing. Code is imported from fortran and to comply with original indexes we actually generate one index more. Also second dimension is 2j+2 instead of 2j+2. elements starting with 0 are useles and should be ignored!
SP	37	sph->co=(ts_double *)calloc(l+1,sizeof(ts_double ));
	38	for(j=0;j<=l;j++){
	39	sph->co[j]=(ts_double )calloc(2j+2,sizeof(ts_double));
074a17	40	}
SP	41
5bb11d	42	sph->l=l;
SP	43
	44	/* Calculate coefficients that will remain constant during all the simulation */
	45	precomputeShCoeff(sph);
	46
074a17	47	return sph;
SP	48	}
	49
	50
eb8605	51	ts_bool sph_free(ts_spharm *sph){
SP	52	int i,j;
632960	53	if(sph==NULL) return TS_FAIL;
074a17	54	for(i=0;i<sph->l;i++){
SP	55	if(sph->ulm[i]!=NULL) free(sph->ulm[i]);
262607	56	if(sph->sumUlm2[i]!=NULL) free(sph->sumUlm2[i]);
074a17	57	if(sph->co[i]!=NULL) free(sph->co[i]);
SP	58	}
79fc9c	59	if(sph->co[sph->l]!=NULL) free(sph->co[sph->l]);
074a17	60	if(sph->co != NULL) free(sph->co);
SP	61	if(sph->ulm !=NULL) free(sph->ulm);
	62
eb8605	63	if(sph->Ylmi!=NULL) {
074a17	64	for(i=0;i<sph->l;i++){
eb8605	65	if(sph->Ylmi[i]!=NULL){
5bb11d	66	for(j=0;j<i*2+1;j++){
eb8605	67	if(sph->Ylmi[i][j]!=NULL) free (sph->Ylmi[i][j]);
SP	68	}
	69	free(sph->Ylmi[i]);
	70	}
074a17	71	}
eb8605	72	free(sph->Ylmi);
074a17	73	}
eb8605	74
074a17	75	free(sph);
SP	76	return TS_SUCCESS;
	77	}
	78
88f451	79	/* Gives you legendre polynomials. Taken from NR, p. 254 */
3b3902	80	ts_double plgndr(ts_int l, ts_int m, ts_double x){
88f451	81	ts_double fact, pll, pmm, pmmp1, somx2;
SP	82	ts_int i,ll;
	83
	84	#ifdef TS_DOUBLE_DOUBLE
	85	if(m<0 \|\| m>l \|\| fabs(x)>1.0)
	86	fatal("Bad arguments in routine plgndr",1);
	87	#endif
	88	#ifdef TS_DOUBLE_FLOAT
	89	if(m<0 \|\| m>l \|\| fabsf(x)>1.0)
	90	fatal("Bad arguments in routine plgndr",1);
	91	#endif
	92	#ifdef TS_DOUBLE_LONGDOUBLE
	93	if(m<0 \|\| m>l \|\| fabsl(x)>1.0)
	94	fatal("Bad arguments in routine plgndr",1);
	95	#endif
	96	pmm=1.0;
	97	if (m>0) {
	98	#ifdef TS_DOUBLE_DOUBLE
	99	somx2=sqrt((1.0-x)*(1.0+x));
	100	#endif
	101	#ifdef TS_DOUBLE_FLOAT
	102	somx2=sqrtf((1.0-x)*(1.0+x));
	103	#endif
	104	#ifdef TS_DOUBLE_LONGDOUBLE
	105	somx2=sqrtl((1.0-x)*(1.0+x));
	106	#endif
	107	fact=1.0;
	108	for (i=1; i<=m;i++){
	109	pmm = -factsomx2;
	110	fact +=2.0;
	111	}
	112	}
	113
	114	if (l == m) return pmm;
	115	else {
	116	pmmp1=x(2m+1)*pmm;
	117	if(l==(m+1)) return(pmmp1);
	118	else {
	119	pll=0; /* so it can not be uninitialized */
	120	for(ll=m+2;ll<=l;ll++){
	121	pll=(x(2ll-1)pmmp1-(ll+m-1)pmm)/(ll-m);
	122	pmm=pmmp1;
	123	pmmp1=pll;
	124	}
	125	return(pll);
	126	}
	127	}
	128	}
	129
	130
9bf6ee	131	/** @brief: Precomputes coefficients that are required for spherical harmonics computations.
523bf1	132
9bf6ee	133	*/
523bf1	134	ts_bool precomputeShCoeff(ts_spharm *sph){
074a17	135	ts_int i,j,al,am;
SP	136	ts_double **co=sph->co;
79fc9c	137	for(i=1;i<=sph->l;i++){
SP	138	al=i;
074a17	139	sph->co[i][i+1]=sqrt((2.0*al+1.0)/2.0/M_PI);
79fc9c	140	for(j=1;j<=i-1;j++){
SP	141	am=j;
008026	142	sph->co[i][i+1+j]=co[i][i+j]*sqrt(1.0/(al-am+1.0)/(al+am));
074a17	143	sph->co[i][i+1-j]=co[i][i+1+j];
523bf1	144	}
79fc9c	145	co[i][2i+1]=co[i][2i]sqrt(1.0/(2.0al));
SP	146	co[i][1]=co[i][2*i+1];
074a17	147	co[i][i+1]=sqrt((2.0*al+1.0)/4.0/M_PI);
523bf1	148	}
SP	149	return TS_SUCCESS;
	150
	151	}
	152
	153
c9d07c	154	/** @brief: Computes Y(l,m,theta,fi)
SP	155	*
	156	* Function calculates Y^l_m for vertex with given (\theta, \fi) coordinates in
	157	* spherical coordinate system.
	158	* @param l is an ts_int argument.
	159	* @param m is an ts_int argument.
	160	* @param theta is ts_double argument.
	161	* @param fi is a ts_double argument.
	162	*
	163	* (Miha's definition that is different from common definition for factor srqt(1/(2pi)) /
88f451	164	ts_double shY(ts_int l,ts_int m,ts_double theta,ts_double fi){
SP	165	ts_double fac1, fac2, K;
	166	int i;
	167
	168	if(l<0 \|\| m>l \|\| m<-l)
	169	fatal("Error using shY function!",1);
	170
	171	fac1=1.0;
af3bad	172	for(i=1; i<=l-abs(m);i++){
88f451	173	fac1 *= i;
SP	174	}
	175	fac2=1.0;
af3bad	176	for(i=1; i<=l+abs(m);i++){
88f451	177	fac2 *= i;
SP	178	}
	179
	180	if(m==0){
	181	K=sqrt(1.0/(2.0*M_PI));
	182	}
	183	else if (m>0) {
	184	K=sqrt(1.0/(M_PI))cos(mfi);
	185	}
	186	else {
	187	//K=pow(-1.0,abs(m))sqrt(1.0/(2.0M_PI))cos(mfi);
	188	if(abs(m)%2==0)
af3bad	189	K=sqrt(1.0/(M_PI))cos(mfi);
88f451	190	else
af3bad	191	K=-sqrt(1.0/(M_PI))cos(mfi);
88f451	192	}
SP	193
632960	194	return Ksqrt((2.0l+1.0)/2.0(ts_double)(fac1/fac2))plgndr(l,abs(m),cos(theta));
88f451	195	}
523bf1	196
SP	197
	198	/* Function transforms coordinates from cartesian to spherical coordinates
	199	* (r,phi, theta). */
	200	ts_bool cart2sph(ts_coord coord, ts_double x, ts_double y, ts_double z){
	201	coord->coord_type=TS_COORD_SPHERICAL;
	202	#ifdef TS_DOUBLE_DOUBLE
	203	coord->e1=sqrt(xx+yy+z*z);
	204	if(z==0) coord->e3=M_PI/2.0;
e9c87e	205	else coord->e3=atan2(sqrt(xx+yy),z);
523bf1	206	coord->e2=atan2(y,x);
SP	207	#endif
	208	#ifdef TS_DOUBLE_FLOAT
	209	coord->e1=sqrtf(xx+yy+z*z);
	210	if(z==0) coord->e3=M_PI/2.0;
	211	else coord->e3=atanf(sqrtf(xx+yy)/z);
	212	coord->e2=atan2f(y,x);
	213	#endif
	214	#ifdef TS_DOUBLE_LONGDOUBLE
	215	coord->e1=sqrtl(xx+yy+z*z);
	216	if(z==0) coord->e3=M_PI/2.0;
	217	else coord->e3=atanl(sqrtl(xx+yy)/z);
	218	coord->e2=atan2l(y,x);
	219	#endif
	220
	221	return TS_SUCCESS;
	222	}
	223
e9c87e	224
SP	225	ts_bool sph2cart(ts_coord *coord){
	226	coord->coord_type=TS_COORD_CARTESIAN;
	227	ts_double x,y,z;
	228
	229	x=coord->e1cos(coord->e2)sin(coord->e3);
	230	y=coord->e1sin(coord->e2)sin(coord->e3);
	231	z=coord->e1*cos(coord->e3);
	232
	233	coord->e1=x;
	234	coord->e2=y;
	235	coord->e3=z;
	236
	237	return TS_SUCCESS;
	238	}
	239
	240
523bf1	241	/* Function returns radius of the sphere with the same volume as vesicle (r0) */
SP	242	ts_double getR0(ts_vesicle *vesicle){
	243	ts_double r0;
	244	#ifdef TS_DOUBLE_DOUBLE
	245	r0=pow(vesicle->volume*3.0/4.0/M_PI,1.0/3.0);
	246	#endif
	247	#ifdef TS_DOUBLE_FLOAT
	248	r0=powf(vesicle->volume*3.0/4.0/M_PI,1.0/3.0);
	249	#endif
	250	#ifdef TS_DOUBLE_LONGDOUBLE
	251	r0=powl(vesicle->volume*3.0/4.0/M_PI,1.0/3.0);
	252	#endif
	253	return r0;
	254	}
	255
	256
	257	ts_bool preparationSh(ts_vesicle *vesicle, ts_double r0){
	258	//TODO: before calling or during the call calculate area of each triangle! Can
	259	//be also done after vertexmove and bondflip //
919555	260	//DONE: in energy calculation! //
523bf1	261	ts_uint i,j;
SP	262	ts_vertex **vtx=vesicle->vlist->vtx;
	263	ts_vertex *cvtx;
	264	ts_triangle *ctri;
	265	ts_double centroid[3];
	266	ts_double r;
	267	for (i=0; i<vesicle->vlist->n; i++){
	268	cvtx=vtx[i];
	269	//cvtx->projArea=4.0M_PI/1447.0(cvtx->xcvtx->x+cvtx->ycvtx->y+cvtx->z*cvtx->z)/r0/r0;
	270	cvtx->projArea=0.0;
	271
	272	/* go over all triangles that have a common vertex i */
	273	for(j=0; j<cvtx->tristar_no; j++){
	274	ctri=cvtx->tristar[j];
	275	centroid[0]=(ctri->vertex[0]->x + ctri->vertex[1]->x + ctri->vertex[2]->x)/3.0;
	276	centroid[1]=(ctri->vertex[0]->y + ctri->vertex[1]->y + ctri->vertex[2]->y)/3.0;
	277	centroid[2]=(ctri->vertex[0]->z + ctri->vertex[1]->z + ctri->vertex[2]->z)/3.0;
	278	/* calculating projArea+= area(triangle)cos(theta) /
	279	#ifdef TS_DOUBLE_DOUBLE
	280	cvtx->projArea = cvtx->projArea + ctri->area(-centroid[0]ctri->xnorm - centroid[1]ctri->ynorm - centroid[2]ctri->znorm)/ sqrt(centroid[0]centroid[0]+centroid[1]centroid[1]+centroid[2]*centroid[2]);
	281	#endif
	282	#ifdef TS_DOUBLE_FLOAT
	283	cvtx->projArea = cvtx->projArea + ctri->area(-centroid[0]ctri->xnorm - centroid[1]ctri->ynorm - centroid[2]ctri->znorm)/ sqrtf(centroid[0]centroid[0]+centroid[1]centroid[1]+centroid[2]*centroid[2]);
	284	#endif
	285	#ifdef TS_DOUBLE_LONGDOUBLE
	286	cvtx->projArea = cvtx->projArea + ctri->area(-centroid[0]ctri->xnorm - centroid[1]ctri->ynorm - centroid[2]ctri->znorm)/ sqrtl(centroid[0]centroid[0]+centroid[1]centroid[1]+centroid[2]*centroid[2]);
	287	#endif
	288	}
	289
	290	cvtx->projArea=cvtx->projArea/3.0;
	291	//we dont store spherical coordinates of vertex, so we have to calculate
	292	//r(i) at this point.
	293	#ifdef TS_DOUBLE_DOUBLE
	294	r=sqrt(cvtx->xcvtx->x+cvtx->ycvtx->y+cvtx->z*cvtx->z);
	295	#endif
	296	#ifdef TS_DOUBLE_FLOAT
	297	r=sqrtf(cvtx->xcvtx->x+cvtx->ycvtx->y+cvtx->z*cvtx->z);
	298	#endif
	299	#ifdef TS_DOUBLE_LONGDOUBLE
	300	r=sqrtl(cvtx->xcvtx->x+cvtx->ycvtx->y+cvtx->z*cvtx->z);
	301	#endif
	302	cvtx->relR=(r-r0)/r0;
3b3902	303	cvtx->solAngle=cvtx->projArea/r/r;
523bf1	304	}
SP	305	return TS_SUCCESS;
	306	}
	307
	308
	309
	310	ts_bool calculateYlmi(ts_vesicle *vesicle){
3b3902	311	ts_int i,j,k;
523bf1	312	ts_spharm *sph=vesicle->sphHarmonics;
SP	313	ts_coord coord=(ts_coord )malloc(sizeof(ts_coord));
	314	ts_double fi, theta;
79048f	315	ts_int m;
074a17	316	ts_vertex *cvtx;
523bf1	317	for(k=0;k<vesicle->vlist->n;k++){
074a17	318	cvtx=vesicle->vlist->vtx[k];
eb8605	319	sph->Ylmi[0][0][k]=sqrt(1.0/4.0/M_PI);
074a17	320	cart2sph(coord,cvtx->x, cvtx->y, cvtx->z);
523bf1	321	fi=coord->e2;
SP	322	theta=coord->e3;
79048f	323	for(i=1; i<sph->l; i++){
523bf1	324	for(j=0;j<i;j++){
79048f	325	m=j+1;
3b3902	326	//Nastudiraj!!!!!
79048f	327	sph->Ylmi[i][j][k]=sph->co[i][m]cos((m-i-1)fi)pow(-1,m-i-1)plgndr(i,abs(m-i-1),cos(theta));
3b3902	328	if(i==2 && j==0){
SP	329	/* fprintf(stderr," ** vtx %d **\n", k+1);
	330	fprintf(stderr,"m-i-1 =%d\n",m-i-1);
	331	fprintf(stderr,"fi =%e\n",fi);
	332	fprintf(stderr,"(m-i-1)fi =%e\n",((ts_double)(m-i-1))fi);
	333	fprintf(stderr,"-2fi =%e\n",-2fi);
	334	fprintf(stderr,"m =%d\n",m);
	335
	336	fprintf(stderr," cos(m-i-1)=%e\n",cos((m-i-1)*fi));
	337	fprintf(stderr," cos(-2fi)=%e\n",cos(-2fi));
	338	fprintf(stderr," sph->co[i][m]=%e\n",sph->co[i][m]);
	339	fprintf(stderr," plgndr(i,abs(m-i-1),cos(theta))=%e\n",plgndr(i,abs(m-i-1),cos(theta)));
	340	*/
	341	}
523bf1	342	}
3b3902	343	//Nastudiraj!!!!!
SP	344	j=i;
	345	m=j+1;
	346	sph->Ylmi[i][j][k]=sph->co[i][m]*plgndr(i,0,cos(theta));
	347	for(j=i+1;j<2*i+1;j++){
79048f	348	m=j+1;
3b3902	349	//Nastudiraj!!!!!
79048f	350	sph->Ylmi[i][j][k]=sph->co[i][m]sin((m-i-1)fi)*plgndr(i,m-i-1,cos(theta));
523bf1	351	}
SP	352	}
	353
	354	}
	355	free(coord);
	356	return TS_SUCCESS;
	357	}
	358
	359
	360
	361	ts_bool calculateUlm(ts_vesicle *vesicle){
	362	ts_uint i,j,k;
	363	ts_vertex *cvtx;
	364	for(i=0;i<vesicle->sphHarmonics->l;i++){
8e58b4	365	for(j=0;j<2*i+1;j++) vesicle->sphHarmonics->ulm[i][j]=0.0;
523bf1	366	}
SP	367
	368	//TODO: call calculateYlmi !!!
	369
	370
	371	for(k=0;k<vesicle->vlist->n; k++){
	372	cvtx=vesicle->vlist->vtx[k];
	373	for(i=0;i<vesicle->sphHarmonics->l;i++){
3b3902	374	for(j=0;j<2*i+1;j++){
eb8605	375	vesicle->sphHarmonics->ulm[i][j]+= cvtx->solAnglecvtx->relRvesicle->sphHarmonics->Ylmi[i][j][k];
523bf1	376	}
SP	377
	378	}
	379	}
	380
	381	return TS_SUCCESS;
	382	}
262607	383
SP	384
	385
	386
	387
	388	ts_bool storeUlm2(ts_vesicle *vesicle){
	389
	390	ts_spharm *sph=vesicle->sphHarmonics;
	391	ts_int i,j;
	392	for(i=0;i<sph->l;i++){
	393	for(j=0;j<2*i+1;j++){
8e58b4	394	/* DEBUG fprintf(stderr,"sph->sumUlm2[%d][%d]=%e\n",i,j,sph->ulm[i][j]* sph->ulm[i][j]); */
fda1ab	395	sph->sumUlm2Old[i][j]+=sph->ulm[i][j]* sph->ulm[i][j];
262607	396	}
SP	397	}
	398	sph->N++;
	399	return TS_SUCCESS;
	400	}
dc77e8	401
SP	402
	403	ts_bool saveAvgUlm2(ts_vesicle *vesicle){
	404
	405	FILE *fh;
267db5	406	char filename[10000];
SP	407	strcpy(filename, command_line_args.path);
fda1ab	408	strcat(filename, "sph2outOld.dat");
267db5	409	fh=fopen(filename, "w");
dc77e8	410	if(fh==NULL){
SP	411	err("Cannot open file %s for writing");
	412	return TS_FAIL;
	413	}
	414
	415	ts_spharm *sph=vesicle->sphHarmonics;
	416	ts_int i,j;
	417	fprintf(fh,"l,\tm,\tulm^2avg\n");
	418	for(i=0;i<sph->l;i++){
	419	for(j=0;j<2*i+1;j++){
fda1ab	420	fprintf(fh,"%d,\t%d,\t%e\n", i, j-i, sph->sumUlm2Old[i][j]/(ts_double)sph->N);
dc77e8	421
SP	422	}
	423	fprintf(fh,"\n");
	424	}
	425	fclose(fh);
	426	return TS_SUCCESS;
	427	}